Copying Armature through Python API
You copied the armature OBJECT, not the armature data.  The copied object referred to the same datablock (armature.data).  If you look at the properties panel in the armature tab (as opposed to the object or materials tab) you will see a [2] next to the name of the armature datablock

Instead:

ao = ob.find_armature()
a2 = ao.data.copy()
a2.transform(conversionMatrix)


This copies the armature datablock instead of the object datablock.